Biochemistry - Proteins

the amide bond between 2 amino acids

peptide bond

link amino acids in proteins

peptide bond

peptide bonds formed by what

condensation of the alpha carboxyl group of one amino acids with the alpha amino group of another amino acid (loss of H2O molecule)

peptide bonds can connect multiple amino acids to make an amino acid polymer called what

polypeptide chain

an amino acid unit in a peptide - the part left over after losing a H from its amino group and an OH from its carboxyl group

residue

the end of a peptide with a free alpha amino group

amino (N) terminal end

the end of a peptide with a free alpha carboxyl group

carboxyl (C) terminal end

what is the placement of the terminal ends when an amino acid sequence of a peptide (protein) is displayed

N terminal end - left

C terminal end - right

short amino acid polymers that generally have fewer than 50 amino acid residues

peptides

amino acid polymers with more than 50 amino acid residues

polypeptides

macromolecule composed of one or more polypeptides

protein

some proteins consist of a single polypeptide chain and some have two or more polypeptides associated ____ ; the subunits can be identical or different

noncovalently

why are proteins important to us?

much of our body is constructed from protein molecules

protein molecules play a vital role in keeping our body working properly (ex. hemoglobin, hormones, antibodies, enzymes)

5 parts of our body composed of mainly protein materials

muscle, cartilage, ligaments, skin, hair

amino acid linear sequence

primary structure of protein

regions of regular repeating conformations of the peptide chain, such as alpha-helices and beta-sheets

secondary structure of protein

the shape of the fully folded polypeptide chain

tertiary structure of protein

arrangement of two or more polypeptide chains into multisubunit molecule

quaternary structure

most _____ are proteins

enzymes

the _____ of a protein represents the linear arrangement of amino acids via peptide bonds

primary structure

how is the primary structure of a protein read

from N-terminus to C-terminus

Primary structure, the amino acid sequence, is specified by

genetic information

what does the primary sequence of a protein dictate

its higher order structures as well as its function

coiled structure around a long central axis, stabilized by intrachain hydrogen bonds

alpha helix (right handed)

structure of the alpha helix

carbonyl oxygen (residue n) is hydrogen bonded to the amide hydrogen of the fourth residue (n+4) further toward the carboxyl terminus

in the alpha helix, all hydrogen bonds are ____ to the helix axis

parallel

how many amino acid residues per turn in the alpha helix?

3.6

in the alpha helix, all the side chains (R) project which way

outward from the helix axis

form when different sections of the polypeptide chain run alongside each other

beta pleated sheets

each individual segment of a beta pleated sheet is referred to as a what

beta strand

each beta strand of a beta pleated sheet is ____

fully extended

how are beta sheets stabilized?

by hydrogen bonds between C=O and -NH on adjacent strands

a polypeptide chain that fold back and forth upon itself, with each section of the chain running in the direction opposite to that of its immediate neighbors

antiparallel beta sheets

which way do the strands run in antiparallel beta sheets

in opposite N- to C- terminal directions

a polypeptide chain that fold back and forth upon itself, with sections of the chain running in the same direction

parallel beta sheets

which way do the strands run in parallel beta sheets

strands run in the same N- to C- terminal direction

results from the folding of a polypeptide chain into a closely-packed three-dimensional structure

tertiary structure

amino acids that are far apart in the primary structure may be brought together in the ____ structure

tertiary

how are tertiary structures stabilized

primary by nonequivalent interactions between side chain

disulfide bridges (-S-S-) are also part of ____ structure

tertiary

shows the overall shape of a protein

space-filling model

easy way to visualize secondary structures

ribbon model

when can proteins have quaternary structure

when it is made up of two or more polypeptides

each polypeptide is called a

protein subunit

refers to the spatial arrangement (organization) of subunits in a protein with more than one polypeptide chain

quaternary structure

subunits in a protein may be _____ or ____ in their amino acid sequence (primary structure)

identical or different

subunits in a protein are held together by what

many weak noncovalent interactions

a single polypeptide chain that has 8 alfa helices

myoglobin (Mb)

myoglobin contains a_____ group

covalently bound heme group

myoglobin is the oxygen storage protein of ____

muscle

why is myoglobin abundant in diving mammals like seals and whales

because they can store oxygen in this form for prolonged periods underwater

tetrameric protein (alfa2beta2) that carries oxygen in the blood

hemoglobin (Hb)

each subunit of hemoglobin contains a ____

heme

the alfa chain of hemoglobin has ____ alpha helices and the beta chain has ____ alpha helices

alfa chain - 7

beta chain - 8

myoglobin has 8 ____ helices

alfa

what is the three dimensional structure of a protein determined by

its primary sequence

any _____ of a given primary sequence will have a unique or near unique structure

isolated protein

______interactions are most important in stabilizing protein structure

noncovalent

why are noncovalent interactions important in stabilizing protein structure

noncovalent bonds help proteins fold, and the folded conformation is much stronger

have polypeptide chains that are folded in a spherical or rounded shape

globular shape

globular proteins have a ____ interior and a ____ surface

hydrophobic interior

hydrophilic surface

globular proteins include what

enzymes, regulatory proteins, and carrier proteins

ex. hemoglobin

globular proteins are water ____

soluble

have polypeptide chains arranged in long strands

fibrous proteins

fibrous proteins provide what

mechanical support

examples of fibrous proteins

keratins - hair and nails

collagen - tendons, skin, bones

fibrous proteins are water ____

insoluble

a protein's ____ is intricately linked to its three dimensional structure

function

disruption of native conformation of a protein, with loss of biological activity by chemical or physical means

denaturation

proteins can be denatured by a variety of means including what

heat

pH extremes

organic solvents

chaotropic agents (urea, guanidine, hydrochloride)

detergents

in each case of protein denaturation no ____ bonds are broken

covalent

denaturing agents disrupt ______, resulting in loss of tertiary and quaternary structure (sometimes secondary structure

noncovalent bonding

8 functions of proteins

structure

catalysts

movement

transport

hormones

protection

storage

regulation

collagen and keratin are the chief constituents of skin, bone, hair, and nails

structure

virtually all reactions in living systems are catalyzed by proteins called enzymes

catalysts

muscles are made up of proteins called myosin and actin

movement

hemoglobin transports oxygen from the lungs to cells; other proteins transport molecules across cell membranes

transport

many hormones are proteins, among them insulin, and human growth hormone

hormones

blood clotting involves the protein fibrinogen; the body uses proteins called antibodies to fight disease

protection

casein in milk and ovalbumin in eggs store nutrients for newborn infants and birds

ferritin, a protein in the liver, stores iron

storage

certain proteins not only control the expression of genes, but also control when gene expression takes place

regulation

which contributes MOST to the primary structure of a protein?

covalent bonds